btllib Namespace Reference

Classes
class	AAHash
class	BlindNtHash
class	BlindSeedNtHash
class	BloomFilter
class	CountingBloomFilter
class	Indexlr
class	KmerBloomFilter
class	KmerCountingBloomFilter
class	NtHash
class	ProcessPipeline
class	RandSeq
class	SeedAAHash
class	SeedBloomFilter
class	SeedNtHash
class	SeqReader
class	SeqWriter

Typedefs
using	SpacedSeed = std::vector<unsigned>
using	CountingBloomFilter8 = CountingBloomFilter<uint8_t>
using	CountingBloomFilter16 = CountingBloomFilter<uint16_t>
using	CountingBloomFilter32 = CountingBloomFilter<uint32_t>
using	KmerCountingBloomFilter8 = KmerCountingBloomFilter<uint8_t>
using	KmerCountingBloomFilter16 = KmerCountingBloomFilter<uint16_t>
using	KmerCountingBloomFilter32 = KmerCountingBloomFilter<uint32_t>
using	PipeId = unsigned long
using	PipelineId = unsigned long

Functions
std::vector< SpacedSeed >	aa_parse_seeds (const std::vector< std::string > &seeds)
std::vector< std::vector< unsigned > >	parse_seeds (const std::vector< std::string > &seed_strings)
void	reverse_complement (std::string &seq)
std::string	get_reverse_complement (const std::string &seq)
std::string	get_time ()
void	log_info (const std::string &msg)
void	log_warning (const std::string &msg)
void	log_error (const std::string &msg)
void	check_info (bool condition, const std::string &msg)
void	check_warning (bool condition, const std::string &msg)
void	check_error (bool condition, const std::string &msg)
std::string	get_strerror ()
void	check_stream (const std::ios &stream, const std::string &name)
void	check_file_accessibility (const std::string &filepath)
std::vector< std::string >	split (const std::string &s, const std::string &delim)
std::string	join (const std::vector< std::string > &s, const std::string &delim)
void	ltrim (std::string &s)
void	ltrim (btllib::CString &s)
void	rtrim (std::string &s)
void	rtrim (btllib::CString &s)
void	trim (std::string &s)
void	trim (btllib::CString &s)
bool	startswith (std::string s, std::string prefix)
bool	endswith (std::string s, std::string suffix)
std::string	get_basename (const std::string &path)
std::string	get_dirname (const std::string &path)
double	sum_phred (const std::string &qual, size_t start_pos=0, size_t len=0)
double	calc_phred_avg (const std::string &qual, size_t start_pos=0, size_t len=0)

Variables
const char	COMPLEMENTS [256]
const char	AMINO_ACIDS [256]
const char	CAPITALS [256]
constexpr const char *	PRINT_COLOR_INFO = "\33[32m"
constexpr const char *	PRINT_COLOR_WARNING = "\33[33m"
constexpr const char *	PRINT_COLOR_ERROR = "\33[31m"
constexpr const char *	PRINT_COLOR_END = "\33[0m"

Detailed Description

Functions for sequence manipulation.

Functions for logging and error checking.

Random utility functions.

Function Documentation

calc_phred_avg()

double btllib::calc_phred_avg	(	const std::string &	qual,
		size_t	start_pos = 0,
		size_t	len = 0 )

Calculate the average phred score of a string, depending on the start position and length.

Parameters

qual	The quality string to calculate the average from.
start_pos	The start position of the substring. Defaults to 0.
len	The length of the substring. Defaults to 0. If 0, the whole string is used.

Returns

The average phred score of the substring.

check_error()

void btllib::check_error	(	bool	condition,
		const std::string &	msg )

Conditionally log error level events. The program exits if the condition is true.

Parameters

condition	If this is true, the message is printed and the program exits.
msg	Message to print.

check_file_accessibility()

void btllib::check_file_accessibility

(

const std::string &

filepath

)

Check whether the file at the given path is accessible (exists, permissions are good, etc.).

Parameters

filepath

Path to the file to check.

check_info()

void btllib::check_info	(	bool	condition,
		const std::string &	msg )

Conditionally log info level events.

Parameters

condition	If this is true, the message is printed.
msg	Message to print.

check_stream()

void btllib::check_stream	(	const std::ios &	stream,
		const std::string &	name )

Check whether the stream is good. Program prints an error message and exits if not.

Parameters

stream	Stream to check goodness of.
name	Name of the stream, e.g. filepath or stdin

check_warning()

void btllib::check_warning	(	bool	condition,
		const std::string &	msg )

Conditionally log warning level events.

Parameters

condition	If this is true, the message is printed.
msg	Message to print.

endswith()

bool btllib::endswith	(	std::string	s,
		std::string	suffix )

Check whether the given string ends with a suffix.

Parameters

s	String to check.
suffix	Suffix to check for.

get_basename()

std::string btllib::get_basename

(

const std::string &

path

)

Equivalent to the GNU implementation of basename, but returns a string copy of the result.

Parameters

path	The path to get basename from.

Returns

The basename of the path.

get_dirname()

std::string btllib::get_dirname

(

const std::string &

path

)

Equivalent to the GNU implementation of dirname, but returns a string copy of the result.

Parameters

path	The path to get dirname from.

Returns

The dirname of the path.

get_reverse_complement()

std::string btllib::get_reverse_complement

(

const std::string &

seq

)

Obtain a reverse complement of the provided sequence. The argument sequence is left untouched.

Parameters

seq	Sequence to reverse complement.

Returns

Reverse complemented sequence.

get_time()

std::string btllib::get_time

(

)

Return current time as a string.

join()

std::string btllib::join	(	const std::vector< std::string > &	s,
		const std::string &	delim )

Join a vector of strings into a single string with a delimiter.

Parameters

s	Vector of strings to join.
delim	Delimiter to join the strings with.

Returns

String with all the components joined.

log_error()

void btllib::log_error

(

const std::string &

msg

)

Log error level events.

Parameters

msg	Message to print.

log_info()

void btllib::log_info

(

const std::string &

msg

)

Log info level events.

Parameters

msg	Message to print.

log_warning()

void btllib::log_warning

(

const std::string &

msg

)

Log warning level events.

Parameters

msg	Message to print.

ltrim()

void btllib::ltrim

(

std::string &

s

)

Trim whitespace on the left side of the given string.

Parameters

s	String to trim, edited in-place.

parse_seeds()

std::vector< std::vector< unsigned > > btllib::parse_seeds ( const std::vector< std::string > & seed_strings )

inline

Parse each spaced seed pattern into lists of don't care positions. Legacy function used in btllib Bloom filters.

reverse_complement()

void btllib::reverse_complement

(

std::string &

seq

)

Reverse complement a sequence in-place.

Parameters

seq	Sequence to reverse complement.

rtrim()

void btllib::rtrim

(

std::string &

s

)

Trim whitespace on the right side of the given string.

Parameters

s	String to trim, edited in-place.

split()

std::vector< std::string > btllib::split	(	const std::string &	s,
		const std::string &	delim )

Split a string into component substrings with a delimiter.

Parameters

s	String to split.
delim	Delimiter to split with.

Returns

Vector of substrings delimited by delim, excluding delimiters themselves.

startswith()

bool btllib::startswith	(	std::string	s,
		std::string	prefix )

Check whether the given string starts with a prefix.

Parameters

s	String to check.
prefix	Prefix to check for.

sum_phred()

double btllib::sum_phred	(	const std::string &	qual,
		size_t	start_pos = 0,
		size_t	len = 0 )

Calculate the sum of the phred scores of a string.

Parameters

qual	The quality string to calculate the sum from.
start_pos	The start position of the substring. Defaults to 0.
len	The length of the substring. Defaults to 0. If 0, the whole string is used.

Returns

The sum of the phred scores of the substring.

trim()

void btllib::trim

(

std::string &

s

)

Trim whitespace on the left and right side of the given string.

Parameters

s	String to trim, edited in-place.